Financial incentives that stimulate energy investments under public–private partnerships are considered scarce public resources, which require deliberate allocation to the most economically justified projects to maximize the social benefits. This study aims to solve the financial incentive allocation problem through a real option-based nonlinear integer programming approach. Real option theory is leveraged to determine the optimal timing and the corresponding option value of providing financial incentives. The ambiguity in the evolution of social benefits, the decision-maker’s attitude toward ambiguity, and the uncertainty in social benefits and incentive costs are all considered. Incentives are offered to the project portfolio that generates the maximum total option value. The project portfolio selection is formulated as a stochastic knapsack problem with random option values in the objective function and random incentive costs in the probabilistic budget constraint. The linear probabilistic budget constraint is subsequently transformed into a nonlinear deterministic one. Finally, the integer non-linear programming problem is solved, and the optimality gap is computed to assess the quality of the optimal solution. A case study is presented to illustrate how the limited financial incentives can be optimally allocated under uncertainty and ambiguity, which demonstrates the efficacy of the proposed method.